From cf0a80b4871235693d07d149f872d010e09ea0c0 Mon Sep 17 00:00:00 2001 From: Alexis CRISCUOLO <alexis.criscuolo@pasteur.fr> Date: Wed, 22 Jul 2020 08:45:14 +0200 Subject: [PATCH] 2.0 --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index b546ad7..1e3a516 100644 --- a/README.md +++ b/README.md @@ -133,12 +133,12 @@ Launch _JolyTree_ without option to read the following documentation: * The option `-c` allows multiple substitutions per character to be accurately estimated when an observed _p_-distance is quite large (e.g. > 0.1; see [Figure 3.1](https://books.google.fr/books?id=3Xc8DwAAQBAJ&pg=PA41) in Nei and Kumar 2000). In such cases, all the _p_-distances _p_ estimated by _mash_ are transformed into proper evolutionary distances _d_. Since _JolyTree_ v2.0, four _p_-distance transformations can be obtained using options `-c` and/or `-a`: <div align="center"> -| transformation | formula | options | notes | -|:------------------------|:------------------------------------------------------------------------|:------------------------------------------------------------|:--------------------------------------------------------------------------------------------------| -| none | _d_ = _p_ | `-c 1 -a $a` with any `$a` > 0 | unaccurate estimate when _p_ > 0.1 | -| Poisson correction | _d_ = - log<sub>_e_</sub>(1 - _p_) | `-a 0` (use `-c 1` to force Poisson correction) | default _p_-distance transformation of _mash_ | -| F81/EI correction | _d_ = -_b_<sub>1</sub> log<sub>_e_</sub>(1 - _p_/_b_<sub>2</sub>) | `-a 0` (use `-c 0` to force F81/EI correction) | formula (4) in [Tamura and Kumar (2002)](https://academic.oup.com/mbe/article/19/10/1727/1258975) | -| F81/EI gamma correction | _d_ = -_ab_<sub>1</sub>[(1 - _p_/_b_<sub>2</sub>)<sup>-1/_a_</sup> - 1] | `-a $a` with specified gamma shape parameter (default: 1.5) | formula (3) in Criscuolo (2020; _submitted_) | +| correction | formula | options | notes | +|:-----------------|:------------------------------------------------------------------------|:--------------------------------------------------------------|:--------------------------------------------------------------------------------------------------| +| none | _d_ = _p_ | `-c 1 -a $a` with any `$a` > 0 | unaccurate estimate when _p_ > 0.1 | +| Poisson | _d_ = - log<sub>_e_</sub>(1 - _p_) | `-a 0` (use `-c 1` to force Poisson correction) | default _p_-distance transformation of _mash_ | +| F81/EI | _d_ = -_b_<sub>1</sub> log<sub>_e_</sub>(1 - _p_/_b_<sub>2</sub>) | `-a 0` (use `-c 0` to force F81/EI correction) | formula (4) in [Tamura and Kumar (2002)](https://academic.oup.com/mbe/article/19/10/1727/1258975) | +| F81/EI + Γ | _d_ = -_ab_<sub>1</sub>[(1 - _p_/_b_<sub>2</sub>)<sup>-1/_a_</sup> - 1] | `-a $a` with specified Γ shape parameter (default: 1.5) | formula (3) in Criscuolo (2020; _submitted_) | </div> -- GitLab